Daniel,
I finally had a chance to run a thorough memory leak test on the
Amber plugin that you were using for your files, and on machine, I see
no leaks after going through a loop loading/analyzing and deleting your
test molecule 600 times. My "analysis" test was just doing an atom
selection and querying the number of selected atoms, but given the
original problem description this seemed adequate to try and reproduce
the problem. This makes me wonder if there leaks in the shared libraries
on your particular Linux machine or something similar. I ran my tests
using the latest test builds of VMD 1.9.3.